Publications
Papers
* corresponding author
25. Masuda Y*, Senoo K.
Iron oxide minerals: promising materials for sustainable rice production via stimulating iron-reducing diazotrophs. 2025. Biosci Biotech Biochem. doi:10.1093/bbb/zbaf156
24. Chaonan Wang, Masuda Y*, Senoo K.
Ammonium Generating Microbial Consortia in Paddy Soil Revealed by DNA-Stable Isotope Probing and Meta-transcriptomics. 2025. doi: 10.3390/microorganisms13071448
23. Lin LY, Feng Z, Asano H, Ohmori Y, Ohba H, Masuda Y, Senoo K, Fujiwara T.
Genome-wide association study identifies key chromosomal regions in rice promoting the enrichment of diazotrophic iron-reducing bacteria in paddy soil. 2025. Plant Soil. doi: 10.1007/s11104-025-07384-9
22. Mise K, Masuda Y, Senoo K, Itoh H.
Betaproteobacterial clade II nosZ activated under high N2O concentrations in paddy soil microcosms. 2025. J Appl Microbiol. doi:10.1093/jambio/lxaf055
21. Okamoto T, Hotta Y, Shinjo R, Masuda Y, Nishirhara A, Sasaki R, Hirai M, Nishiwaki R, Miyado S, Sugiura D, Kondo M.
Unelongated Stems are an Active Nitrogen-Fixing Site in Rice Stems Supported by Both Sugar and Methane Under Low Nitrogen Conditions. 2025. Rice. doi: 10.1186/s12284-025-00757-9
20. Xu Z, Hattori S, Masuda Y*, Toyoda S, Koba K, Yu P, Yoshida N, Du ZJ, Senoo K.
Unprecedented N 2 O production by nitrate-ammonifying Geobacteraceae with distinctive N2O isotopocule signatures. 2024. mBio. doi: 10.1128/mbio.02540-24
19. Masuda Y*, Mise K, Xu Z, Zhang Z, Shiratori Y, Senoo K, Itoh H.
Global soil metagenomics reveals distribution and predominance of Deltaproteobacteria in nitrogen-fixing microbiome. 2024. Microbiome. doi: 10.1186/s40168-024-01812-1
18. Masuda Y*, Chihara M, Senoo K.
Ferrihydrite Addition Activated Geobacteraceae, the Most Abundant Iron-reducing Diazotrophs, and Suppressed Methanogenesis by Heterogeneous Methanogens in Xylan-amended Paddy Soil Microcosms. 2024. Microbes Environ. doi: 10.1264/jsme2.ME24028
17. Itoh H, Sugisawa Y, Mise K, Xu Z, Kuniyasu M, Ushijima N, Kawano K, Kobayashi E, Shiratori Y, Masuda Y, Senoo K.
Mesoterricola silvestris gen. nov., sp. nov., Mesoterricola sediminis sp. nov., Geothrix oryzae sp. nov., Geothrix edaphica sp. nov., Geothrix rubra sp. nov., and Geothrix limicola sp. nov., six novel members of Acidobacteriota isolated from soils. 2024. Int J Sys Environ Microbiol.
16. Zhang Z, Masuda Y*, Xu Z, Shiratori Y, Ohba H, Senoo K.
Active Nitrogen Fixation by Iron-Reducing Bacteria in Rice Paddy Soil and Its Further Enhancement by Iron Application. 2023. Appl Sci. doi: 10.3390/app13148156
15. Masuda Y, Satoh S, Miyamoto R, Takano R, Ishii K, Ohba H, Shiratori Y, Senoo K.
Biological nitrogen fixation in the long-term nitrogen-fertilized and unfertilized paddy fields, with special reference to diazotrophic iron-reducing bacteria. 2023. Arc Microbiol. doi: 10.1007/s00203-023-03631-8
14. Itoh H, Xu Z, Mise K, Masuda Y, Ushijima N, Hayakawa C, Shiratori Y, Senoo K.
Anaeromyxobacter oryzae sp. nov., Anaeromyxobacter diazotrophicus sp. nov. and Anaeromyxobacter paludicola sp. nov., isolated from paddy soils. 2022. Int J Syst Environ Microbiol. doi: 10.1099/ijsem.0.005546
13. Shen W, Long Y, Qiu Z, Gao N, Masuda Y, Itoh H, Ohba H, Shiratori Y, Rajasekar A, Senoo K.
Investigation of Rice Yields and Critical N Losses from Paddy Soil under Different N Fertilization Rates with Iron Application. 2022. Int J Environ Res Public Health. doi: 10.3390/ijerph19148707
12. Mise K, Masuda Y, Senoo K, Itoh H.
Undervalued Pseudo- nifH Sequences in Public Databases Distort Metagenomic Insights into Biological Nitrogen Fixers. 2021. mSphere. doi: 10.1128/msphere.00785-21
11. Xu Z, Masuda Y*, Wang X, Ushijima N, Shiratori Y, Senoo K, Itoh H.
Genome-based taxonomic rearrangement of the order Geobacterales including the description of Geomonas azotofixans sp. nov. and Geomonas diazotrophicus sp. nov. 2021. Front Microbiol. doi: 10.3389/fmicb.2021.737531
10. Zhang Z, Xu Z, Masuda Y*, Wang X, Ushijima N, Shiratori Y, Senoo K, Itoh H.
Geomesophilobacter sediminis gen. nov., sp. nov., Geomonas propionica sp. nov. and Geomonas anaerohicana sp. nov., three novel members in the family Geobacterecace isolated from river sediment and paddy soil. 2021. Syst Appl Microbiol., doi: 10.1016/j.syapm.2021.126233.
9. Shen H, Shiratori Y, Ohta S, Masuda Y, Isobe K, Senoo K.
Mitigating N2O emissions from agricultural soils with fungivorous mites. 2021. ISME J., doi: 10.1038/s41396-021-00948-4.
8. Masuda Y*, Shiratori Y, Ohba H, Ishida T, Takano R, Satoh S, Shen W, Gao N, Itoh H, Senoo K.
Enhancement of the nitrogen-fixing activity of paddy soils owing to iron application. 2021. Soil Sci Plant Nut., doi: 10.1080/00380768.2021.1888629.
7. Itoh H, Xu Z, Masuda Y, Ushijima N, Hayakawa C, Shiratori Y, Senoo K.
Geomonas silvestris sp. nov., Geomonas paludis sp. nov. and Geomonas limicola sp. nov., isolated from terrestrial environments, and emended description of the genus Geomonas. 2020. Int J Syst Evol Microbiol., 71: 004607. doi:10.1099/ijsem.0.004607.
6. Masuda Y, Yamanaka H, Xu Z, Shiratori Y, Aono T, Amachi S, Senoo K, Itoh H.
Diazotrophic Anaeromyxobacter isolated from soils. 2020. Appl Environ Microbiol., 86: e00956-20. doi: 10.1128/AEM.00956-20.
5. Xu Z, Masuda Y*, Hayakawa C, Ushijima N, Shiratori Y, Senoo K, Itoh H.
Description of Three Novel Members in the Family Geobacteraceae, Oryzomonas japonicum gen. nov., sp. nov., Oryzomonas sagensis sp. nov., and Oryzomonas ruber sp. nov. 2020. Microorganisms, 8:634. doi: 10.3390/microorganisms8050634.
4. Xu Z, Masuda Y*, Itoh H, Shiratori Y, Senoo K.
Geomonas oryzae gen. nov., sp. nov., Geomonas edaphica sp. nov., Geomonas ferrireducens sp. nov., Geomonas terrae sp. nov., Four Ferric-Reducing Bacteria Isolated from Paddy Soil, and Reclassification of Three Species of the Genus Geobacter as Members of the Genus Geomonas gen. nov. 2019. Front Microbiol., 10:2201. doi:10.3389/fmicb.2019.02201.
3. Masuda Y*, Matsumoto T, Isobe K, Senoo K.
Denitrification in paddy soil as a cooperative process of different nitrogen oxide reducers, revealed by metatranscriptomic analysis of denitrification-induced soil microcosm. 2019. Soil Sci Plant Nut., 65: 342-345. doi: 10.1080/00380768.2019.1622401.
2．Masuda Y*, Itoh H, Shiratori Y, Senoo K.
Metatranscriptomic insights into microbial consortia driving methane metabolism in paddy soils. 2018. Soil Sci Plant Nut., 64:455-464. doi: 10.1080/00380768.2018.1457409.
1．Masuda Y, Itoh H, Shiratori Y, Isobe K, Otsuka S, Senoo K.
Predominant but previously-overlooked prokaryotic drivers of reductive nitrogen transformation in paddy soils, revealed by metatranscriptomics. 2017. Microbes Environ., 32:180-183. doi: 10.1264/jsme2.ME16179.
Books
12. 増田曜子
『サステイナブルな農業を支える！？鉄還元菌』日本微生物生態学会誌、2025、40巻2号
11. 増田曜子
『微生物と鉄を利用した水田土壌における窒素肥沃度向上』化学工学、2025、89巻4号
10. 増田曜子
『メタトランスクリプトーム解析による水田土壌微生物の新機能発見とその応用-メタン生成・消去や窒素固定を担う微生物-』作物生産と土づくり、2024、56巻1号
9. Masuda Y, Shen W, Senoo K.
Discovery of previously overlooked microbial drivers of nitrogen fixation in paddy soil, iron-reducing bacteria, and application to low nitrogen input agriculture. 2024. Nitrogen Cycling and Soil Health, Progress in Soil Science book series published by Springer Nature.
8.増田曜子
『オミックス技術が切り開く土壌肥料学 4. 水田土壌メタトランスクリプトミクス—窒素・炭素循環を駆動する土壌微生物群の真相解明—』土壌肥料学会誌、2023、94巻4号
7.増田曜子、妹尾啓史
『鉄で土を肥やす』科学（岩波書店）、2023
6. 妹尾啓史、増田曜子
『水田土壌における鉄還元菌窒素固定の発見と低窒素農業への応用の試み —オミクス解析からサステイナブル農業へ— 』日本土壌肥料学雑誌、2023、94巻3号
5．妹尾啓史、増田曜子、伊藤英臣、白鳥豊、大峽広智、Xu Zhenxing、山中遥加、石田敬典、高野諒、佐藤咲良、Shen Weishou
『水田土壌における鉄還元菌窒素固定の学術的基盤解明と低窒素農業への応用：低炭素社会の実現を目指して』土と微生物、2021
4．増田曜子、伊藤英臣
『土壌圏の新たな微生物生態をあぶり出すメタトランスクリプトーム解析』アグリバイオ、2021、5巻 1号
3．増田曜子、伊藤英臣、白鳥豊、妹尾啓史
『水田土壌における鉄還元菌窒素固定の発見と応用 〜オミクス解析から低窒素農業へ〜』化学と生物、2020、58巻 3号
2．増田曜子
『水田土壌の鉄還元菌のもう一つの顔―窒素肥沃度を支えるキープレーヤー―』土と微生物、2018、72巻 1号
1．増田曜子
『メタトランスクリプトーム解析によって導かれた, 還元的窒素変換反応への鉄還元菌の寄与』日本微生物生態学会誌、2017、32巻 1号
